A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/pacvar analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2024-11-12, 20:42 UTC
based on data in:
/Users/tanyajain/Desktop/nextflow_fun/pacvar/work/e2/756759a1464cc857e8f88481545fbb
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| Workflow | Nextflow | 24.04.4 |
| nf-core/pacvar | v0.1.0 |
nf-core/pacvar Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/pacvar
Methods
Data was processed using nf-core/pacvar v0.1.0 of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.04.4 (Di Tommaso et al., 2017) with the following command:
nextflow run main.nf -profile test,docker --outdir out -resumeReferences
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/pacvar Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/pacvar
Core Nextflow options
- runName
- suspicious_kalam
- containerEngine
- docker
- launchDir
- /Users/tanyajain/Desktop/nextflow_fun/pacvar
- workDir
- /Users/tanyajain/Desktop/nextflow_fun/pacvar/work
- projectDir
- /Users/tanyajain/Desktop/nextflow_fun/pacvar
- userName
- tanyajain
- profile
- test,docker
- configFiles
- N/A
Input/output options
- input
- https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/samplesheet_longread_puretarget.csv
- outdir
- out
Reference genome options
- genome
- GATK.GRCh38
- fasta
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
- fasta_fai
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
- dbsnp
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
- dbsnp_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
- dict
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
Institutional config options
- config_profile_name
- Test profile
- config_profile_description
- Minimal test dataset to check pipeline function
Pre-processing options that are not workflow specific
- barcodes
- https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/barcodes_D01.fasta
- intervals
- https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/c9orf72.bed
General workflow options
- workflow
- repeat
